Metagenomic analysis of sedimentary archives reveals ‘historical’ antibiotic resistance genes diversity increased over recent decades in the environment

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Abstract Antibiotic Resistance Genes (ARGs) are widespread in freshwater environments and represent a concealed threat to public health and aquatic eco-system safety. To date, only a limited number of studies have investigated the historical distribution of ARGs and their hosts through the analysis of freshwater sedimentary archives. This research gap constrains our comprehensive of the mechanisms underlying natural bacterial resistance formation during pre-antibiotic era (prior to the 1940s) and the development of human-induced bacterial resistance in post-antibiotic era (since the 1940s). In this study, we examined the vertical distribution patterns of ARGs and their associated hosts within a sedimentary core from a eutrophic lake, employing shotgun sequencing methodology. The findings revealed a marked increase in ARG diversity during post-antibiotic era, and the predominant ARG types identified included those conferring resistance to multidrug, bacitracin, macrolide–lincosamide–streptogramin, beta-lactam, tetracycline, fluoroquinolone, glycopeptide and aminoglycoside, collectively accounting for 78.3%–85.6% of total ARG abundance. A total of 127 ARG subtypes were identified in samples, and 48 ARG subtypes shared across vertical sediment resistome profile with two of them, bacA and bcrA, occurring only in post-antibiotic era. Further, 137 metagenome-assembled genomes (83 species belonging to 12 phyla) were identified as ARG hosts, mainly belonging to the phyla Proteobacteria, Nitrospirota, Chloroflexota, Bacteroidota, Actinobacteriota, Cyanobacteria, and Firmicutes. Significant correlation was found between the diversity of ARG and the concentrations of organic matter and heavy metals, suggesting a common source of contamination. Aside the fact that human-induced eutrophication is a forcing factor acting in parallel to increase ARGs releases in water systems, both being indicators of increased urbanization in the catchment, eutrophication may significantly increase bacterial activity, thereby facilitating the spread of antibiotic-resistant bacteria in environment. This study reveals the marked increased in ARG diversity with the onset of antibiotic use by human societies with potential impact of aquatic ecosystem.